Plant Transcription Factors: Methods and Protocols

Section I. Introduction

1. MADS & More: Transcription Factors that Shape the Plant

Rainer Melzer and G?nter Thei en

Section II. Identification of Transcription Factors

2. In Silico Mining and PCR Based Approaches to Transcription Factor Discovery in Non-Model Plants: Gene Discovery of the WRKY Transcription Factors in Conifers

Jun-Jun Liu and Yu Xiang

3. Isolation of Plant Transcription Factors Using a Yeast One-Hybrid System

Tatiana Pyvovarenko and Sergiy Lopato

4. A Transposon Based Activation Tagging System for Gene Function Discovery in Arabidopsis

Nayelli Marsch-Mart?nez

Section III. Functional Verification

5. CRES-T, An Effective Gene Silencing System Utilizing Chimeric Repressors

Nobutaka Mitsuda, Kyoko Matsui, Miho Ikeda, Masaru Nakata, Yoshimi Ooshima, Yukari Nagatoshi, and Masaru Ohme-Takagi

6. Analysis of a Transcription Factor Using Transient Assay in Arabidopsis Protoplasts

Yuji Iwata, Mi-Hyun Lee, and Nozomu Koizumi

7. Microarray-Based Identification of Transcription Factor Target Genes

Maartje Gorte, Anneke Horstman, Robert B. Page, Renze Heidstra, Arnold Stromberg, and Kim Boutilier

Section IV. Protein-Protein Interaction and Other Means for Activity Control

8. Yeast Protein-Protein Interaction Assays and Screens

Stefan de Folter and Richard G.H. Immink

9. Mapping Functional Domains of transcription factors

Ling Zhu and Enamul Huq

10. Bimolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts

Sitakanta Pattanaik, Joshua R. Werkman, and Ling Yuan

11. Isolation of transcription factor complexes from Arabidopsis cell suspension cultures by tandem affinity purification

Jelle Van Leene, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Jan Geerinck, Gert Van Isterdael, Erwin Witters, and Geert De Jaeger

12. Assaying Transcription Factor Stability

Jasmina Kurepa and Jan A. Smalle

13. How to assess the intercellular trafficking of transcription factors

Munawar Ahmad, Won Kyong Cho, Yeonggil Rim, Lijun Huang, and Jae-Yean Kim

Section V. Protein-DNA Interaction

14. SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space

Chenglin Chai, Zidian Xie, and Erich Grotewold

15. Footprinting and Missing Nucleoside Analysis of Transcription Factor-DNA Complexes

Ivana L. Viola and Daniel H. Gonzalez

16. Chromatin immunoprecipitation to verify or to identify In Vivo protein-DNA interactions

Yumei Zheng and Sharyn E. Perry

17. Visualizing and characterizing In Vivo DNA-Binding Events and Direct Target Genes of Plant Transcription Factors

Jose M. Mui?o, Gerco C. Angenent, and Kerstin Kaufmann

18. Mapping In Vivo Protein-DNA Interactions in Plants by DamID, a DNA Adenine Methylation-Based Method

Sophie Germann and Val?rie Gaudin

Section VI. Engineering Metablolic Pathways using Transcription Factors

19. Directed Evolution through DNA Shuffling for the Improvement and Understanding of Genes and Promoters

Joshua R. Werkman, Sitakanta Pattanaik, and Ling Yuan